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Fluorine in PDB 7db8: Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845:
6.1.1.20;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845, PDB code: 7db8 was solved by M.Xu, X.Zhang, L.Xu, S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.64 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 278.005, 297.814, 65.901, 90, 90, 90
R / Rfree (%) 16.8 / 18.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845 (pdb code 7db8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845, PDB code: 7db8:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7db8

Go back to Fluorine Binding Sites List in 7db8
Fluorine binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:39.3
occ:1.00
 F21 A:H2R404 0.0 39.3 1.0
C20 A:H2R404 1.3 30.2 1.0
F23 A:H2R404 2.1 38.4 1.0
F22 A:H2R404 2.1 38.3 1.0
C17 A:H2R404 2.4 29.2 1.0
C16 A:H2R404 2.8 30.0 1.0
CD1 A:LEU219 3.3 25.0 1.0
CD2 A:LEU219 3.5 22.9 1.0
C18 A:H2R404 3.6 26.9 1.0
CG A:LEU219 3.8 25.9 1.0
CB A:LEU219 4.0 20.8 1.0
N15 A:H2R404 4.1 33.3 1.0
CB A:GLN180 4.2 29.2 1.0
CG2 A:VAL286 4.3 29.1 1.0
CB A:ALA305 4.6 23.0 1.0
CG A:GLN180 4.7 32.7 1.0
C19 A:H2R404 4.7 22.1 1.0
CB A:VAL286 4.8 27.0 1.0
CG1 A:VAL290 4.8 21.1 1.0
C14 A:H2R404 4.9 29.5 1.0
CD2 A:LEU146 5.0 32.1 1.0
CD1 A:ILE181 5.0 25.4 1.0

Fluorine binding site 2 out of 3 in 7db8

Go back to Fluorine Binding Sites List in 7db8
Fluorine binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:38.3
occ:1.00
 F22 A:H2R404 0.0 38.3 1.0
C20 A:H2R404 1.3 30.2 1.0
F21 A:H2R404 2.1 39.3 1.0
F23 A:H2R404 2.1 38.4 1.0
C17 A:H2R404 2.4 29.2 1.0
C18 A:H2R404 2.8 26.9 1.0
CD2 A:LEU146 3.2 32.1 1.0
C16 A:H2R404 3.6 30.0 1.0
CG1 A:VAL290 3.9 21.1 1.0
CG2 A:VAL286 4.1 29.1 1.0
C19 A:H2R404 4.1 22.1 1.0
CB A:PHE257 4.2 22.2 1.0
CG2 A:VAL290 4.5 22.9 1.0
O A:PHE257 4.6 23.8 1.0
CD1 A:ILE181 4.6 25.4 1.0
CD1 A:PHE257 4.6 20.3 1.0
CG A:PHE257 4.7 24.0 1.0
CB A:VAL290 4.7 31.2 1.0
CG A:LEU146 4.7 30.6 1.0
N15 A:H2R404 4.7 33.3 1.0
C14 A:H2R404 4.9 29.5 1.0
CB A:VAL286 5.0 27.0 1.0

Fluorine binding site 3 out of 3 in 7db8

Go back to Fluorine Binding Sites List in 7db8
Fluorine binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Phenylalanyl-Trna Synthetase in Complex with Compound Pf-3845 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:38.4
occ:1.00
 F23 A:H2R404 0.0 38.4 1.0
C20 A:H2R404 1.3 30.2 1.0
F21 A:H2R404 2.1 39.3 1.0
F22 A:H2R404 2.1 38.3 1.0
C17 A:H2R404 2.4 29.2 1.0
C16 A:H2R404 3.2 30.0 1.0
C18 A:H2R404 3.2 26.9 1.0
CD2 A:LEU146 3.5 32.1 1.0
O A:SER177 3.7 25.8 1.0
CB A:SER177 3.7 34.0 1.0
CB A:GLN180 3.8 29.2 1.0
CD1 A:ILE181 3.9 25.4 1.0
CA A:SER177 4.1 29.1 1.0
OG A:SER177 4.2 38.8 1.0
C A:SER177 4.3 24.2 1.0
CG1 A:ILE181 4.3 28.0 1.0
N15 A:H2R404 4.4 33.3 1.0
C19 A:H2R404 4.5 22.1 1.0
N A:ILE181 4.6 23.5 1.0
CG A:GLN180 4.7 32.7 1.0
CG A:LEU146 4.7 30.6 1.0
CD2 A:LEU219 4.8 22.9 1.0
CA A:GLN180 4.8 27.6 1.0
OE1 A:GLN180 4.8 33.9 1.0
C A:GLN180 4.8 27.2 1.0
C14 A:H2R404 4.9 29.5 1.0
CG1 A:VAL290 5.0 21.1 1.0

Reference:

H.Wang, M.Xu, C.A.Engelhart, X.Zhang, B.Yan, M.Pan, Y.Xu, S.Fan, R.Liu, L.Xu, L.Hua, D.Schnappinger, S.Chen. Re-Discovery of Pf-3845 As A New Chemical Scaffold Inhibiting Phenylalanyl-Trna Synthetase in Mycobacterium Tuberculosis . J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
PubMed: 33397709
DOI: 10.1074/JBC.RA120.016477
Page generated: Tue Jul 15 19:06:08 2025

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